Porphobilinogen deaminase (P06983)

Identification
Name:Porphobilinogen deaminase
Synonyms:
  • PBG
  • Hydroxymethylbilane synthase
  • HMBS
  • Pre-uroporphyrinogen synthase
Gene Name:hemC
Enzyme Class:
Biological Properties
General Function:Involved in hydroxymethylbilane synthase activity
Specific Function:Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps
Cellular Location:Not Available
SMPDB Pathways:
KEGG Pathways:
KEGG Reactions:
4.0Thumb+1.0Thumb ↔ 1.0Thumb+4.0Thumb
4.0Porphobilinogen + 1.0Water ↔ 1.0Hydroxymethylbilane + 4.0Ammonia
ReactionCard
4.0Thumb+1.0Thumb → 1.0Thumb+4.0Thumb
4.0Porphobilinogen + 1.0Water → 1.0Hydroxymethylbilane + 4.0Ammonia
ReactionCard
EcoCyc Reactions:
4.0Thumb+1.0Thumb ↔ 1.0Thumb+4.0Thumb
4.0Porphobilinogen + 1.0Water ↔ 1.0Hydroxymethylbilane + 4.0Ammonia
ReactionCard
1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb+1.0Thumb
1.0Water + 1.0Porphobilinogen ↔ 1.0Hydrogen ion + 1.0Ammonia + 1.0Hydroxymethylbilane
ReactionCard
4.0Thumb+1.0Thumb → 1.0Thumb+4.0Thumb
4.0Porphobilinogen + 1.0Water → 1.0Hydroxymethylbilane + 4.0Ammonia
ReactionCard
Complex Reactions:
1.0Thumb+4.0Thumb → 1.0Thumb+4.0Thumb
1.0Water + 4.0Porphobilinogen → 1.0Hydroxymethylbilane + 4.0Ammonium
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB00051AmmoniaMetaboCard
ECMDB21186AmmoniumMetaboCard
ECMDB01137HydroxymethylbilaneMetaboCard
ECMDB00245PorphobilinogenMetaboCard
ECMDB00494WaterMetaboCard
GO Classification:
Function
catalytic activity
hydroxymethylbilane synthase activity
transferase activity
transferase activity, transferring alkyl or aryl (other than methyl) groups
Process
biosynthetic process
cellular biosynthetic process
heterocycle biosynthetic process
macromolecule metabolic process
macromolecule modification
metabolic process
peptidyl-pyrromethane cofactor linkage
post-translational protein modification
protein modification process
protein-cofactor linkage
tetrapyrrole biosynthetic process
Gene Properties
Blattner:b3805
Gene OrientationCounterclockwise
Centisome Percentage:85.95
Left Sequence End3987848
Right Sequence End3988789
Gene Sequence:
>942 bp
ATGAAGCTGATACGCGGCATACATAATCTCAGCCAGGCCCCGCAAGAAGGGTGTGTGCTG
ACTATTGGTAATTTCGACGGCGTGCATCGCGGTCATCGCGCGCTGTTACAGGGCTTGCAG
GAAGAAGGGCGCAAGCGCAACTTACCGGTGATGGTGATGCTTTTTGAACCTCAACCACTG
GAACTGTTTGCTACCGATAAAGCCCCGGCAAGACTGACCCGGCTGCGGGAAAAACTGCGT
TACCTTGCAGAGTGTGGCGTTGATTACGTGCTGTGCGTGCGTTTCGACAGGCGTTTCGCG
GCGTTAACCGCGCAAAATTTCATCAGCGATCTTCTGGTGAAGCATTTGCGCGTAAAATTT
CTTGCCGTAGGTGATGATTTCCGCTTTGGCGCTGGTCGTGAAGGCGATTTCTTGTTATTA
CAGAAAGCTGGCATGGAATACGGCTTCGATATCACCAGTACGCAAACTTTTTGCGAAGGT
GGCGTGCGCATCAGCAGCACCGCCGTGCGTCAGGCCCTTGCGGATGACAATCTGGCTCTG
GCAGAGAGTTTACTGGGGCACCCGTTTGCCATCTCCGGGCGTGTAGTCCACGGTGATGAA
TTAGGGCGCACTATAGGTTTCCCGACGGCGAATGTACCGCTGCGCCGTCAGGTTTCCCCG
GTGAAAGGGGTTTATGCGGTAGAAGTGCTGGGCCTCGGTGAAAAGCCGTTACCCGGCGTG
GCAAACATCGGAACACGCCCAACGGTTGCCGGTATTCGCCAGCAGCTGGAAGTGCATTTG
TTAGATGTTGCAATGGACCTTTACGGTCGCCATATACAAGTAGTGCTGCGTAAAAAAATA
CGCAATGAGCAGCGATTTGCGTCGCTGGACGAACTGAAAGCGCAGATTGCGCGTGATGAA
TTAACCGCCCGCGAATTTTTTGGGCTAACAAAACCGGCTTAA
Protein Properties
Pfam Domain Function:
Protein Residues:313
Protein Molecular Weight:33851
Protein Theoretical pI:5
PDB File:2YPN
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Porphobilinogen deaminase
MLDNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVILDTPLAKVGGKG
LFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALP
AGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLE
SRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEG
GCQVPIGSYAELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAR
EILAEVYNGDAPA
References
External Links:
ResourceLink
Uniprot ID:P06983
Uniprot Name:HEM3_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:85674289
PDB ID:2YPN
Ecogene ID:EG10429
Ecocyc:EG10429
ColiBase:b3805
Kegg Gene:b3805
EchoBASE ID:EB0424
CCDB:HEM3_ECOLI
BacMap:49176416
General Reference:
  • Alefounder, P. R., Abell, C., Battersby, A. R. (1988). "The sequence of hemC, hemD and two additional E. coli genes." Nucleic Acids Res 16:9871. Pubmed: 3054815
  • Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Daniels, D. L., Plunkett, G. 3rd, Burland, V., Blattner, F. R. (1992). "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Science 257:771-778. Pubmed: 1379743
  • Hadener, A., Alefounder, P. R., Hart, G. J., Abell, C., Battersby, A. R. (1990). "Investigation of putative active-site lysine residues in hydroxymethylbilane synthase. Preparation and characterization of mutants in which (a) Lys-55, (b) Lys-59 and (c) both Lys-55 and Lys-59 have been replaced by glutamine." Biochem J 271:487-491. Pubmed: 2122889
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Jordan, P. M., Thomas, S. D., Warren, M. J. (1988). "Purification, crystallization and properties of porphobilinogen deaminase from a recombinant strain of Escherichia coli K12." Biochem J 254:427-435. Pubmed: 3052434
  • Jordan, P. M., Woodcock, S. C. (1991). "Mutagenesis of arginine residues in the catalytic cleft of Escherichia coli porphobilinogen deaminase that affects dipyrromethane cofactor assembly and tetrapyrrole chain initiation and elongation." Biochem J 280 ( Pt 2):445-449. Pubmed: 1747120
  • Lander, M., Pitt, A. R., Alefounder, P. R., Bardy, D., Abell, C., Battersby, A. R. (1991). "Studies on the mechanism of hydroxymethylbilane synthase concerning the role of arginine residues in substrate binding." Biochem J 275 ( Pt 2):447-452. Pubmed: 2025226
  • Louie, G. V., Brownlie, P. D., Lambert, R., Cooper, J. B., Blundell, T. L., Wood, S. P., Warren, M. J., Woodcock, S. C., Jordan, P. M. (1992). "Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site." Nature 359:33-39. Pubmed: 1522882
  • Miller, A. D., Hart, G. J., Packman, L. C., Battersby, A. R. (1988). "Evidence that the pyrromethane cofactor of hydroxymethylbilane synthase (porphobilinogen deaminase) is bound to the protein through the sulphur atom of cysteine-242." Biochem J 254:915-918. Pubmed: 3196304
  • Miller, A. D., Packman, L. C., Hart, G. J., Alefounder, P. R., Abell, C., Battersby, A. R. (1989). "Evidence that pyridoxal phosphate modification of lysine residues (Lys-55 and Lys-59) causes inactivation of hydroxymethylbilane synthase (porphobilinogen deaminase)." Biochem J 262:119-124. Pubmed: 2510713
  • Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K., Blattner, F. R., Chaudhuri, R. R., Glasner, J. D., Horiuchi, T., Keseler, I. M., Kosuge, T., Mori, H., Perna, N. T., Plunkett, G. 3rd, Rudd, K. E., Serres, M. H., Thomas, G. H., Thomson, N. R., Wishart, D., Wanner, B. L. (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34:1-9. Pubmed: 16397293
  • Thomas, S. D., Jordan, P. M. (1986). "Nucleotide sequence of the hemC locus encoding porphobilinogen deaminase of Escherichia coli K12." Nucleic Acids Res 14:6215-6226. Pubmed: 3529035
  • Trotot, P., Sismeiro, O., Vivares, C., Glaser, P., Bresson-Roy, A., Danchin, A. (1996). "Comparative analysis of the cya locus in enterobacteria and related gram-negative facultative anaerobes." Biochimie 78:277-287. Pubmed: 8874804